- using R Under development (unstable) (2024-07-26 r86926)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-14 (GCC) 14.1.0
GNU Fortran (GCC) 14.1.0
- running under: Fedora Linux 36 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘ATQ/DESCRIPTION’ ... OK
- this is package ‘ATQ’ version ‘0.2.0’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘ATQ’ can be installed ... [10s/11s] OK
See the install log for details.
- checking package directory ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [14s/19s] OK
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [54s/56s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [32s/33s] OK
Running ‘testthat.R’ [32s/32s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [303s/309s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘ATQ_Guide.Rmd’ using rmarkdown
* installing *source* package ‘ATQ’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ATQ)
** Processing: /data/gannet/ripley/R/packages/tests-devel/ATQ.Rcheck/vign_test/ATQ/vignettes/ATQ_Guide_files/figure-html/epidemicSimulation-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 27516 bytes
Input file size = 27630 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21761
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21761
Output IDAT size = 21761 bytes (5755 bytes decrease)
Output file size = 21839 bytes (5791 bytes = 20.96% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/ATQ.Rcheck/vign_test/ATQ/vignettes/ATQ_Guide_files/figure-html/epidemicSimulation-2.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 27646 bytes
Input file size = 27760 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21436
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21436
Output IDAT size = 21436 bytes (6210 bytes decrease)
Output file size = 21514 bytes (6246 bytes = 22.50% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/ATQ.Rcheck/vign_test/ATQ/vignettes/ATQ_Guide_files/figure-html/epidemicSimulation-3.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 25848 bytes
Input file size = 25962 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20264
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20264
Output IDAT size = 20264 bytes (5584 bytes decrease)
Output file size = 20342 bytes (5620 bytes = 21.65% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/ATQ.Rcheck/vign_test/ATQ/vignettes/ATQ_Guide_files/figure-html/epidemicSimulation-4.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 25635 bytes
Input file size = 25749 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20152
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20152
Output IDAT size = 20152 bytes (5483 bytes decrease)
Output file size = 20230 bytes (5519 bytes = 21.43% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/ATQ.Rcheck/vign_test/ATQ/vignettes/ATQ_Guide_files/figure-html/epidemicSimulation-5.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 25100 bytes
Input file size = 25214 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19541
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19541
Output IDAT size = 19541 bytes (5559 bytes decrease)
Output file size = 19619 bytes (5595 bytes = 22.19% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/ATQ.Rcheck/vign_test/ATQ/vignettes/ATQ_Guide_files/figure-html/epidemicSimulation-6.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26451 bytes
Input file size = 26565 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21150
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21150
Output IDAT size = 21150 bytes (5301 bytes decrease)
Output file size = 21228 bytes (5337 bytes = 20.09% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/ATQ.Rcheck/vign_test/ATQ/vignettes/ATQ_Guide_files/figure-html/epidemicSimulation-7.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29165 bytes
Input file size = 29279 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22790
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22790
Output IDAT size = 22790 bytes (6375 bytes decrease)
Output file size = 22868 bytes (6411 bytes = 21.90% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/ATQ.Rcheck/vign_test/ATQ/vignettes/ATQ_Guide_files/figure-html/epidemicSimulation-8.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26622 bytes
Input file size = 26736 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20541
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20541
Output IDAT size = 20541 bytes (6081 bytes decrease)
Output file size = 20619 bytes (6117 bytes = 22.88% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/ATQ.Rcheck/vign_test/ATQ/vignettes/ATQ_Guide_files/figure-html/epidemicSimulation-9.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 25993 bytes
Input file size = 26107 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20085
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20085
Output IDAT size = 20085 bytes (5908 bytes decrease)
Output file size = 20163 bytes (5944 bytes = 22.77% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/ATQ.Rcheck/vign_test/ATQ/vignettes/ATQ_Guide_files/figure-html/epidemicSimulation-10.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26776 bytes
Input file size = 26890 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21166
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21166
Output IDAT size = 21166 bytes (5610 bytes decrease)
Output file size = 21244 bytes (5646 bytes = 21.00% decrease)
Quitting from lines 162-183 [metrics] (ATQ_Guide.Rmd)
Error: processing vignette 'ATQ_Guide.Rmd' failed with diagnostics:
unused arguments (ScYr = 2:10, yr.weights = c(2:10)/sum(c(2:10)))
--- failed re-building ‘ATQ_Guide.Rmd’
SUMMARY: processing the following file failed:
‘ATQ_Guide.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... OK
- checking HTML version of manual ... OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 1 ERROR